X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=8b8f9e39b083d9d4329ff500f335d9f4f04cb786;hb=2bb51be6ba6a3fa741f2131d328cf21c395b506a;hp=6849b880bd34fc20b74d720b86c299451be71802;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 6849b88..8b8f9e3 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -42,6 +42,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			cutoff = "1.0";
 		}
 		
+		//set default value for cutoff
+		if (commandName == "dist.seqs") {	cutoff = "1.0";		}
+
 		string key, value;		
 		//reads in parameters and values
 		if((optionText != "") && (commandName != "help")){
@@ -80,10 +83,21 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "filter")		{ filter = value;		}
 				if (key == "soft")		    { soft = value;		    }
 				if (key == "scale")			{ scale = value;		}
+				if (key == "ends" )			{ ends = value;			}
+				if (key == "processors" )	{ processors = value;	}
+				if (key == "size" )         { size = value;         }
 				
 
 				
 
+				if (key == "template")		{ templatefile = value;	}
+				if (key == "search")		{ search = value;		}
+				if (key == "ksize")			{ ksize = value;		}
+				if (key == "align")		    { align = value;		}
+				if (key == "match")			{ match = value;		}
+				if (key == "mismatch")		{ mismatch = value;	    }
+				if (key == "gapopen")		{ gapopen = value;		}
+				if (key == "gapextend" )	{ gapextend = value;	}
 				
 				if (key == "line") {//stores lines to be used in a set
 					lines.clear();
@@ -144,10 +158,18 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "filter")		{ filter = value;		}
 			if (key == "soft")		    { soft = value;		    }
 			if (key == "scale")			{ scale = value;		}
-
-			
-			
-
+			if (key == "ends" )			{ ends = value;			}
+			if (key == "processors" )	{ processors = value;	}
+			if (key == "size" )         { size = value;         }
+
+			if (key == "template")		{ templatefile = value;	}
+			if (key == "search")		{ search = value;		}
+			if (key == "ksize")			{ ksize = value;		}
+			if (key == "align")		    { align = value;		}
+			if (key == "match")			{ match = value;		}
+			if (key == "mismatch")		{ mismatch = value;	    }
+			if (key == "gapopen")		{ gapopen = value;		}
+			if (key == "gapextend" )	{ gapextend = value;	}
 
 			if (key == "line") {//stores lines to be used in a vector
 				lines.clear();
@@ -181,7 +203,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 		//input defaults for calculators
 		if (commandName == "collect.single") {
 
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow-shen"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -197,7 +219,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "summary.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow-shen"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -211,6 +233,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
+		if (commandName == "dist.seqs") {
+			if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
+			Estimators.clear();
+			splitAtDash(calc, Estimators); 
+		}
 		if (commandName == "venn") {
 			if ((calc == "default") || (calc == "")) { 
 				if (format == "list") { calc = "sobs"; }
@@ -278,17 +305,34 @@ string GlobalData::getTrump()			{   return trump;       }
 string GlobalData::getSoft()			{   return soft;		}
 string GlobalData::getFilter()			{   return filter;		}
 string GlobalData::getScale()			{	return scale;		}
+string GlobalData::getEnds()			{   return ends;		}
+string GlobalData::getProcessors()		{	return processors;	}
+string GlobalData::getSize()            {   return size;        }
 
 void GlobalData::setListFile(string file)	{	listfile = file;	inputFileName = file;}
 void GlobalData::setRabundFile(string file)	{	rabundfile = file;	inputFileName = file;}
 void GlobalData::setSabundFile(string file)	{	sabundfile = file;	inputFileName = file;}
 void GlobalData::setPhylipFile(string file)	{	phylipfile = file;    inputFileName = file;}
 void GlobalData::setColumnFile(string file)	{	columnfile = file;    inputFileName = file;}
+string GlobalData::getTemplateFile()	{	return templatefile;}
+string GlobalData::getSearch()			{	return search;		}
+string GlobalData::getKSize()			{	return ksize;		}
+string GlobalData::getAlign()			{	return align;		}
+string GlobalData::getMatch()			{	return match;		}
+string GlobalData::getMismatch()		{	return mismatch;	}
+string GlobalData::getGapopen()			{	return gapopen;		}
+string GlobalData::getGapextend()		{	return gapextend;	}
+
+void GlobalData::setGroupFile(string file)		{	groupfile = file;	}
+void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file; fileroot = file;}
 void GlobalData::setNameFile(string file)		{	namefile = file;		}
 void GlobalData::setFormat(string Format)		{	format = Format;		}
 void GlobalData::setRandomTree(string Random)	{	randomtree = Random;	}
 void GlobalData::setGroups(string g)			{	groups = g;				}
 void GlobalData::setCalc(string Calc)			{	calc = Calc;			}
+void GlobalData::setEnds(string e)				{   ends = e;				}
+void GlobalData::setProcessors(string p)		{	processors = p;			}
+
 
 /*******************************************************/
 
@@ -318,6 +362,7 @@ void GlobalData::clear() {
 	clustalfile		=   "";
 	treefile		=	"";
 	sharedfile		=	"";
+	templatefile	=	"";
 	cutoff			=	"10.00";
 	format			=	"";
 	precision		=	"100";
@@ -338,8 +383,17 @@ void GlobalData::clear() {
 	trump           =   "";		
 	filter          =   "";		
 	soft            =   "";	
-	scale			=	"log10";	    
-
+	scale			=	"log10";
+	ends			=   "T";  //yes
+	processors		=	"1";
+	size            =   "1000";
+	search			=	"suffix";
+	ksize			=	"7";
+	align			=	"blast";
+	match			=	"1.0";
+	mismatch		=	"-1.0";
+	gapopen			=	"-5.0";
+	gapextend		=	"-2.0";
 }
 
 //*******************************************************/
@@ -359,6 +413,16 @@ void GlobalData::reset() {
 	abund			=   "10";
 	step			=	"0.01";
 	form			=	"integral";
+	ends			=   "T";
+	processors		=	"1";
+	size            =   "1000";
+	search			=	"suffix";
+	ksize			=	"7";
+	align			=	"blast";
+	match			=	"1.0";
+	mismatch		=	"-1.0";
+	gapopen			=	"-5.0";
+	gapextend		=	"-2.0";
 }
 /*******************************************************/